Active maintenance of CD8+T cell naïvety through regulation of global genome architecture

SUMMARY The differentiation of naïve CD8 + cytotoxic T lymphocytes (CTLs) into effector and memory states results in large scale changes in transcriptional and phenotypic profiles. Little is known about how large-scale changes in genome organisation reflect or underpin these transcriptional programs. We utilised Hi-C to map changes in the spatial organisation of long-range genome contacts within naïve, effector and memory virus-specific CD8 + T cells. We observed that the architecture of the naive CD8 + T cell genome was distinct from effector and memory genome configurations with extensive changes within discrete functional chromatin domains. However, deletion of the BACH2 or SATB1 transcription factors was sufficient to remodel the naïve chromatin architecture and engage transcriptional programs characteristic of differentiated cells. This suggests that the chromatin architecture within naïve CD8 + T cells is preconfigured to undergo autonomous remodelling upon activation, with key transcription factors restraining differentiation by actively enforcing the unique naïve chromatin state. One Sentence Summary CD8 + T cell naïvety is actively maintained by transcription factors that enforce a distinct, naïve chromatin architecture. Highlights CD8 + T cell differentiation states are underscored by distinct chromatin looping architectures. Chromatin loops juxtapose CTL state appropriate enhancers, transcription factors and genes. Effector and memory CTLs have similar genome architectures, explaining rapid memory recall. CTL differentiation is restrained by BACH2 and SATB1, which enforce a naïve loop architecture.